Invoice doubling

Our billing staff wrongly use the same invoice number for two different purchases and on the basis of invoices e way bill taken and goods moved to the concerend party.While filing the GSTR 1 the mistake is understood. what can i do. Both the bill has to taken the E way Bill. If i change one party invoice and upload the the detail in gstr 1. any problem arrise with cross checking with e way bill to sales tax department.